Molecular electronics promises the ultimate level of miniaturization of computers and other machines as organic molecules are the smallest known physical objects with nontrivial structure and function. But despite the plethora of molecular switches, memories, and motors developed during the almost 50-years long history of molecular electronics, mass production of molecular computers is still an elusive goal. This is mostly due to the lack of scalable nanofabrication methods capable of rapidly producing complex structures (similar to silicon chips or living cells) with atomic precision and a small number of defects. Living nature solves this problem by using linear polymer templates encoding large volumes of structural information into sequence of hydrogen bonded end groups which can be efficiently replicated and which can drive assembly of other molecular components into complex supramolecular structures. In this paper, we propose a nanofabrication method based on a class of photosensitive polymers inspired by these natural principles, which can operate in concert with UV photolithography used for fabrication of current microelectronic processors. We believe that such a method will enable a smooth transition from silicon toward molecular nanoelectronics and photonics. To demonstrate its feasibility, we performed a computational screening of candidate molecules that can selectively bind and therefore allow the deterministic assembly of molecular components. In the process, we unearthed trends and design principles applicable beyond the immediate scope of our proposed nanofabrication method, e.g., to biologically relevant DNA analogues and molecular recognition within hydrogen-bonded systems.

Institute of Physics Czech Academy of Sciences Na Slovance 2 182 00 Prague Czech Republic

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Zhang K.; Wang C.; Zhang M.; Bai Z.; Xie F.-F.; Tan Y.-Z.; Guo Y.; Hu K.-J.; Cao L.; Zhang S.; Tu X.; Pan D.; Kang L.; Chen J.; Wu P.; Wang X.; Wang J.; Liu J.; Song Y.; Wang G.; et al. A Gd@C82 Single-Molecule Electret. Nat. Nanotechnol. 2020, 15, 1019–1024. 10.1038/s41565-020-00778-z. PubMed DOI

Zhang J. L.; Zhong J. Q.; Lin J. D.; Hu W. P.; Wu K.; Xu G. Q.; Wee A. T. S.; Chen W. Towards Single Molecule Switches. Chem. Soc. Rev. 2015, 44, 2998–3022. 10.1039/C4CS00377B. PubMed DOI

Aviram A.; Ratner M. A. Molecular Rectifiers. Chem. Phys. Lett. 1974, 29, 277–283. 10.1016/0009-2614(74)85031-1. DOI

Kushmerick J. Molecular Transistors Scrutinized. Nature 2009, 462, 994–995. 10.1038/462994a. PubMed DOI

Luo Y.; Collier C. P.; Jeppesen J. O.; Nielsen K. A.; DeIonno E.; Ho G.; Perkins J.; Tseng H.-R.; Yamamoto T.; Stoddart J. F.; Heath J. R. Two-Dimensional Molecular Electronics Circuits. ChemPhysChem. 2002, 3, 519–525. 10.1002/1439-7641(20020617)3:6<519::AID-CPHC519>3.0.CO;2-2. PubMed DOI

Green J. E.; Choi J. W.; Boukai A.; Bunimovich Y.; Johnston-Halperin E.; DeIonno E.; Luo Y.; Sheriff B. A.; Xu K.; Shin Y. S.; Tseng H.-R.; Stoddart J. F.; Heath J. R. A 160-Kilobit Molecular Electronic Memory Patterned at 1011 Bits per Square Centimetre. Nature 2007, 445, 414–417. 10.1038/nature05462. PubMed DOI

Browne W. R.; Feringa B. L. Making Molecular Machines Work. Nat. Nanotechnol. 2006, 1, 25–35. 10.1038/nnano.2006.45. PubMed DOI

Li J.; Ballmer S. G.; Gillis E. P.; Fujii S.; Schmidt M. J.; Palazzolo A. M. E.; Lehmann J. W.; Morehouse G. F.; Burke M. D. Synthesis of Many Different Types of Organic Small Molecules Using One Automated Process. Science 2015, 347, 1221–1226. 10.1126/science.aaa5414. PubMed DOI PMC

Jaroš A.; Bonab E. F.; Straka M.; Foroutan-Nejad C. Fullerene-Based Switching Molecular Diodes Controlled by Oriented External Electric Fields. J. Am. Chem. Soc. 2019, 141, 19644–19654. 10.1021/jacs.9b07215. PubMed DOI

Castellanos M. A.; Dodin A.; Willard A. P. On the Design of Molecular Excitonic Circuits for Quantum Computing: the Universal Quantum Gates. Phys. Chem. Chem. Phys. 2020, 22, 3048–3057. 10.1039/C9CP05625D. PubMed DOI

Doležal J.; Canola S.; Hapala P.; de Campos Ferreira R. C.; Merino P.; Švec M. Real Space Visualization of Entangled Excitonic States in Charged Molecular Assemblies. ACS Nano 2022, 16, 1082–1088. 10.1021/acsnano.1c08816. PubMed DOI

Liljeroth P.; Repp J.; Meyer G. Current-Induced Hydrogen Tautomerization and Conductance Switching of Naphthalocyanine Molecules. Science 2007, 317, 1203–1206. 10.1126/science.1144366. PubMed DOI

Gross L.; Mohn F.; Moll N.; Liljeroth P.; Meyer G. The Chemical Structure of a Molecule Resolved by Atomic Force Microscopy. Science 2009, 325, 1110–1114. 10.1126/science.1176210. PubMed DOI

Gross L.; Schuler B.; Pavliček N.; Fatayer S.; Majzik Z.; Moll N.; Peña D.; Meyer G. Atomic Force Microscopy for Molecular Structure Elucidation. Angew. Chem., Int. Ed. 2018, 57, 3888–3908. 10.1002/anie.201703509. PubMed DOI

Steurer W.; Fatayer S.; Gross L.; Meyer G. Probe-Based Measurement of Lateral Single-Electron Transfer Between Individual Molecules. Nat. Commun. 2015, 6, 8353.10.1038/ncomms9353. PubMed DOI PMC

Fatayer S.; Albrecht F.; Zhang Y.; Urbonas D.; Peña D.; Moll N.; Gross L. Molecular Structure Elucidation with Charge-State Control. Science 2019, 365, 142–145. 10.1126/science.aax5895. PubMed DOI

Leinen P.; Esders M.; Schütt K. T.; Wagner C.; Müller K.-R.; Tautz F. S. Autonomous Robotic Nanofabrication with Reinforcement Learning. Sci. Adv. 2020, 6, eabb698710.1126/sciadv.abb6987. PubMed DOI PMC

Clair S.; de Oteyza D. G. Controlling a Chemical Coupling Reaction on a Surface: Tools and Strategies for On-Surface Synthesis. Chem. Rev. (Washington, DC, U. S.) 2019, 119, 4717–4776. 10.1021/acs.chemrev.8b00601. PubMed DOI PMC

Slater A. G.; Perdigão L. M. A.; Beton P. H.; Champness N. R. Surface-Based Supramolecular Chemistry Using Hydrogen Bonds. Acc. Chem. Res. 2014, 47, 3417–3427. 10.1021/ar5001378. PubMed DOI

Corpinot M. K.; Bučar D.-K. A Practical Guide to the Design of Molecular Crystals. Cryst. Growth Des. 2019, 19, 1426–1453. 10.1021/acs.cgd.8b00972. DOI

Conti S.; Cecchini M. Predicting Molecular Self-Assembly at Surfaces: a Statistical Thermodynamics and Modeling Approach. Phys. Chem. Chem. Phys. 2016, 18, 31480–31493. 10.1039/C6CP05249E. PubMed DOI

Shang J.; Wang Y.; Chen M.; Dai J.; Zhou X.; Kuttner J.; Hilt G.; Shao X.; Gottfried J. M.; Wu K. Assembling Molecular Sierpiński Triangle Fractals. Nat. Chem. 2015, 7, 389–393. 10.1038/nchem.2211. PubMed DOI

Abel G. R.; Cao B. H.; Hein J. E.; Ye T. Covalent, sequence-specific attachment of long DNA molecules to a surface using DNA-templated click chemistry. Chem. Commun. 2014, 50, 8131–8133. 10.1039/C4CC02900C. PubMed DOI

Li X.; Liu D. R. DNA-Templated Organic Synthesis: Nature’s Strategy for Controlling Chemical Reactivity Applied to Synthetic Molecules. Angew. Chem., Int. Ed. 2004, 43, 4848–4870. 10.1002/anie.200400656. PubMed DOI

Rothemund P. W. K. Folding DNA to Create Nanoscale Shapes and Patterns. Nature 2006, 440, 297–302. 10.1038/nature04586. PubMed DOI

Hong F.; Zhang F.; Liu Y.; Yan H. DNA Origami: Scaffolds for Creating Higher Order Structures. Chem. Rev. (Washington, DC, U. S.) 2017, 117, 12584–12640. 10.1021/acs.chemrev.6b00825. PubMed DOI

Dey S.; Fan C.; Gothelf K. V.; Li J.; Lin C.; Liu L.; Liu N.; Nijenhuis M. A. D.; Saccà B.; Simmel F. C.; Yan H.; Zhan P. DNA Origami. Nat. Rev. Methods Primers 2021, 1, 13.10.1038/s43586-020-00009-8. DOI

Zhan P.; Peil A.; Jiang Q.; Wang D.; Mousavi S.; Xiong Q.; Shen Q.; Shang Y.; Ding B.; Lin C.; Ke Y.; Liu N. Recent Advances in DNA Origami-Engineered Nanomaterials and Applications. Chem. Rev. (Washington, DC, U. S.) 2023, 123, 3976–4050. 10.1021/acs.chemrev.3c00028. PubMed DOI PMC

Richter A.; Haapasilta V.; Venturini C.; Bechstein R.; Gourdon A.; Foster A. S.; Kühnle A. Diacetylene Polymerization on a Bulk Insulator Surface. Phys. Chem. Chem. Phys. 2017, 19, 15172–15176. 10.1039/C7CP01526G. PubMed DOI

Okawa Y.; Akai-Kasaya M.; Kuwahara Y.; Mandal S. K.; Aono M. Controlled Chain Polymerisation and Chemical Soldering for Single-Molecule Electronics. Nanoscale 2012, 4, 3013–3028. 10.1039/c2nr30245d. PubMed DOI

Repp J.; Meyer G.; Stojković S. M.; Gourdon A.; Joachim C. Molecules on Insulating Films: Scanning-Tunneling Microscopy Imaging of Individual Molecular Orbitals. Phys. Rev. Lett. 2005, 94, 026803.10.1103/PhysRevLett.94.026803. PubMed DOI

Kaiser K.; Lieske L.-A.; Repp J.; Gross L. Charge-State Lifetimes of Single Molecules on Few Monolayers of NaCl. Nat. Commun. 2023, 14, 4988.10.1038/s41467-023-40692-1. PubMed DOI PMC

Lu Y.; Liu M.; Lent C. Molecular Quantum-Dot Cellular Automata: from Molecular Structure to Circuit Dynamics. J. Appl. Phys. 2007, 102, 034311.10.1063/1.2767382. DOI

Pigot C.; Dumur F. Recent Advances of Hierarchical and Sequential Growth of Macromolecular Organic Structures on Surface. Materials 2019, 12, 662.10.3390/ma12040662. PubMed DOI PMC

Treier M.; Pignedoli C. A.; Laino T.; Rieger R.; Müllen K.; Passerone D.; Fasel R. Surface-Assisted Cyclodehydrogenation Provides a Synthetic Route towards Easily Processable and Chemically Tailored Nanographenes. Nat. Chem. 2011, 3, 61–67. 10.1038/nchem.891. PubMed DOI

Fan Q.; Luy J.-N.; Liebold M.; Greulich K.; Zugermeier M.; Sundermeyer J.; Tonner R.; Gottfried J. M. Template-Controlled On-Surface Synthesis of a Lanthanide Supernaphthalocyanine and Its Open-Chain Polycyanine Counterpart. Nat. Commun. 2019, 10, 5049.10.1038/s41467-019-13030-7. PubMed DOI PMC

Fan Q.; Dai J.; Wang T.; Kuttner J.; Hilt G.; Gottfried J. M.; Zhu J. Confined Synthesis of Organometallic Chains and Macrocycles by Cu-O Surface Templating. ACS Nano 2016, 10, 3747–3754. 10.1021/acsnano.6b00366. PubMed DOI

Bansal A.; Kaushik S.; Kukreti S. Non-Canonical DNA Structures: Diversity and Disease Association. Front. Genet. 2022, 13, 959258.10.3389/fgene.2022.959258. PubMed DOI PMC

D’Ascenzo L.; Auffinger P. A Comprehensive Classification and Nomenclature of Carboxyl-Carboxyl(ate) Supramolecular Motifs and Related Catemers: Implications for Biomolecular Systems. Acta Crystallogr., Sect. B: Struct. Sci., Cryst. Eng. Mater. 2015, 71, 164–175. 10.1107/S205252061500270X. PubMed DOI PMC

van der Lubbe S. C. C.; Fonseca Guerra C. The Nature of Hydrogen Bonds: A Delineation of the Role of Different Energy Components on Hydrogen Bond Strengths and Lengths. Chem. - Asian J. 2019, 14, 2760–2769. 10.1002/asia.201900717. PubMed DOI PMC

Hanwell M. D.; Curtis D. E.; Lonie D. C.; Vandermeersch T.; Zurek E.; Hutchison G. R. Avogadro: an Advanced Semantic Chemical Editor, Visualization, and Analysis Platform. J. Cheminf. 2012, 4, 17.10.1186/1758-2946-4-17. PubMed DOI PMC

Rappe A. K.; Casewit C. J.; Colwell K. S.; Goddard III W. A.; Skiff W. M. UFF, a Full Periodic Table Force Field for Molecular Mechanics and Molecular Dynamics Simulations. J. Am. Chem. Soc. 1992, 114, 10024–10035. 10.1021/ja00051a040. DOI

Hourahine B.; Aradi B.; Blum V.; Bonafé F.; Buccheri A.; Camacho C.; Cevallos C.; Deshaye M. Y.; Dumitricǎ T.; Dominguez A.; Ehlert S.; Elstner M.; van der Heide T.; Hermann J.; Irle S.; Kranz J. J.; Köhler C.; Kowalczyk T.; Kubař T.; Lee I. S.; et al. DFTB+, a Software Package for Efficient Approximate Density Functional Theory Based Atomistic Simulations. J. Chem. Phys. 2020, 152, 124101.10.1063/1.5143190. PubMed DOI

Řezáč J. Empirical Self-Consistent Correction for the Description of Hydrogen Bonds in DFTB3. J. Chem. Theory Comput. 2017, 13, 4804–4817. 10.1021/acs.jctc.7b00629. PubMed DOI

Smith D. G. A.; Burns L. A.; Simmonett A. C.; Parrish R. M.; Schieber M. C.; Galvelis R.; Kraus P.; Kruse H.; Di Remigio R.; Alenaizan A.; James A. M.; Lehtola S.; Misiewicz J. P.; Scheurer M.; Shaw R. A.; Schriber J. B.; Xie Y.; Glick Z. L.; Sirianni D. A.; O’Brien J. S.; et al. PSI4 1.4: Open-Source Software for High-Throughput Quantum Chemistry. J. Chem. Phys. 2020, 152, 184108.10.1063/5.0006002. PubMed DOI PMC

Becke A. D. Density-Functional Thermochemistry. III. The Role of Exact Exchange. J. Chem. Phys. 1993, 98, 5648–5652. 10.1063/1.464913. DOI

Grimme S.; Antony J.; Ehrlich S.; Krieg H. A Consistent and Accurate Ab Initio Parametrization of Density Functional Dispersion Correction (DFT-D) for the 94 Elements H-Pu. J. Chem. Phys. 2010, 132, 154104.10.1063/1.3382344. PubMed DOI

van Duijneveldt F. B.; van Duijneveldt-van de Rijdt J. G. C. M.; van Lenthe J. H. State of the Art in Counterpoise Theory. Chem. Rev. (Washington, DC, U. S.) 1994, 94 (7), 1873–1885. 10.1021/cr00031a007. DOI

Burns L. A.; Faver J. C.; Zheng Z.; Marshall M. S.; Smith D. G. A.; Vanommeslaeghe K.; MacKerell A. D. Jr; Merz K. M. Jr; Sherrill C. D. The BioFragment Database (BFDb): An Open-Data Platform for Computational Chemistry Analysis of Noncovalent Interactions. J. Chem. Phys. 2017, 147, 161727.10.1063/1.5001028. PubMed DOI PMC

Jurečka P.; Šponer J.; Černý J.; Hobza P. Benchmark Database of Accurate (MP2 and CCSD(T) Complete Basis Set Limit) Interaction Energies of Small Model Complexes, DNA Base Pairs, and Amino Acid Pairs. Phys. Chem. Chem. Phys. 2006, 8, 1985–1993. 10.1039/B600027D. PubMed DOI

Radiation and DNA Origami Nanotechnology: Probing Structural Integrity at the Nanoscale